Has anyone ever wondered what would've happened had "A Canterlot Wedding" given Rarity top billing. Here's the most likely answer. Just be grateful it was Twilight who had the older brother from Celestia's plot.
Notably, Rarity was absent from Luna Eclipsed. So, what happened? Was she just tired and went to bed for the evening? Was it as Lauren Faust said and that her scene was cut due to time constraints and redundancy? Or...
At least two of the many, many alternate endings to the infamous Cupcakes has the events all just being a fanfic written by one of the Mane Cast. Another has it all being just an Alfred Hitchcock play.
Ponies Play D&D. The initial story of Applejack playing her first Dungeons & Dragons game after everyone else has gotten addicted to it is funny enough, but then it hits a whole new level when the CMC find the gamebooks and each of the mane cast takes a turn as DM.
In The Best Night Ever, Prince Blueblood is utterly confounded by Pinkie Pie, who, despite him being trapped in a "Groundhog Day" Loop, finds himself dealing with something new every time he gets to her.
Blueblood: I - eh - what? What? You didn't ask that last time!
Pinkie Pie: I didn't? Heeeey! What do you mean 'last time?'
Blueblood: I'm repeating the same day over and over. The last time I talked to you, you said something different.
Pinkie Pie: That sounds like me, alright!
Also highly amusing, the part where the Royal Guardsman can't tell if he's supposed to be rescuing Trixie from the Diamond Dogs, or if he's supposed to be rescuing the Diamond Dogs from Trixie.
Canon!Luna greeting at the Gala instead of Celestia. Traditional Royal Canterlot Voice and all.
The Worst Bakers in Equestria has plenty, but one that combines this with awesome is Trixie's semi-semi-final baking attempt. The sheer over-the-topness of it as Trixie's personal Doom Magnet levels of bad luck actually animates her baking attempt into a ravening dough-monster, forcing her to duel it into submission. Commentators Spike and Pinkie Pie are at a complete loss of words over it, and by the end of it, the entire audience in perfect synchronization reset their mouths after they had been dropped in awe.
The Elements of Gaming: In chapter 8, Rainbow Dash and Applejack go into rivalry-mode while playing Burnout, only for them and everyone else in the race to be thoroughly trounced by an unknown (the others being easily identified as Hoops, Score, Dumbbell, and Scootaloo) player with the screen-name of Muffin_Master (you can probably see where this is going). Muffin_Master, naturally, turns out to be none other than Ditzy "Derpy Hooves" Doo.
Also from that chapter: Rarity's reaction to Scootaloo being one of the players, because Scootaloo had told her that she and Sweetie Belle were going to go study.
Rarity: Oh Girls... Do go on without me, would you please? I do believe I've got... problems to take care of. Three very hyperactive problems.
Twilight becoming angry because Pinkie bluescreened the computer from spamming too many Nod militants. Let's just say that her enraged Rapidash form wasn't a good idea to use in the library…
You could probably guess how annoying it was to hear "Fighters arm up!" as she spam builded them.
Along with that: Rarity annihilating the AI opponent when they attacked her perfectly constructed base.
Or Dash facing down 2 hard AIs.
Or in the first chapter, the mane cast having problems with Halo: Reach's legendary difficulty.
Like Twilight starting to swear like Princess Clara when she kept getting killed at a certain point.
In Chapter 2, Twilight and company get to test out Gears of War. She expects Rainbow Dash and Applejack to love it, and they do... until Pinkie starts playing, and gleefully uses the chainsaw bayonet on an enemy, which makes everypony else lose their lunch.
Then comes chapter 3.5, in which Twilight gets hooked on Tetris and plays so well that Pinkie literally shits a pile of bricks while watching her.
The Birds and the Bees, with the mane six each giving their own version of The Talk to the CMC. The punchline everyone's undoubtedly waiting for when they finally ask Pinkie Pie is completely worth the buildup.
Like Fine Wine may be highly explicit material, but as you'd expect from the author of Romance Reports, it has a few funny moments as well, one of the best being Rarity's reaction upon seeing Spike's Exotic Equipment for the first time.
Pinkie Pie Discovers Coffee The real laughs come from the fact that it's not Pinkie Pie that goes nuts after drinking coffee, but Twilight Sparkle.
Suddenly, Twilight became a living ball of energy, exploding up into the air and launching straight for the Cakes. They were taken off guard as she tackled them to the ground, her pupils shrinking as she became the horror they were afraid of.
The fanfic Estrus has a lengthy conversation between five of the Mane Six over how they should break the news to Twilight about the symptoms of heat she's feeling. note She's actually already figured it out - she just hadn't heard it referred to as "in heat" before, only knowing it as "estrous cycle". It contains a lot of hilarious details of how each of them learned about the facts of life and how each chooses to deal with the symptoms. Applejack ends up calling "Too Much Information" on the conversation when Pinkie Pie and Fluttershy start comparing vibrators.
The same author's Fluffershy, in which Hilarity Ensues after Pinkie finds a porn DVD in Mr. Cake's collection with what she recognises as Fluttershy's butt on the cover. The rest of the Mane Six find out about it - except Rainbow, who already had three copies on various formats - and when Fluttershy walks in on them watching her scene, she attempts to commit seppukuwith Angel's carrot.
Strong Bad: "Wait, you’re not Marzipan! Who is this? You mean there’s actually someone else who has an answering machine? Well that’s a load of crap. Although you sound pretty hot. Mmm yeah, hey there, baby. Wanna go out with the one and only Strong Bad? I mean, it’s not like you’re a purple horse or anything."
Homestar Runner: "Whoa, Marzipan! What happened to your voice? I mean, you sound different. Like, did you turn yourself into a talking, purple unicorn or something? Because that’s great! I always wanted a unicorn girlfriend for me to break up with!"
Whom the Princesses Would Destroy, a fantastically written Lower Deck Fic about the Equestrian Civil Service, which feels like if Terry Pratchett or Douglas Adams had written an episode of The West Wing about magical talking ponies. When the A-plot unfolds, the bureaucrats who manage the day-to-day tasks of government are thrown into a panic and scramble to mitigate the political crapstorm that arises when Twilight Sparkle comes by for a surprise visit.
"Quem reginae volunt perdere, dementant prius." — Classical Equestrian proverb, roughly translated: "Whom the princesses would destroy, they first drive mad." Their royal highnesses could not be reached for comment regarding how often this must have occurred to warrant its own proverb.
Dotted Line, the Cabinet Secretary, finds that the library tower where Twilight lived before moving to Ponyville has been covered in four feet of custard, thanks to Princess Luna letting a spell get out of control in a food fight with her sister. When he asks if the inside is filled with custard too, he's assured that it isn't. There's no room on account of all the jam.
Peachy: It worked for us. Twenty-five years since he first stole me away from that low-life mugger I was with, and I haven't looked back.
Andrew Joshua Talon's Hands has many moments of humor in it, but this tropers favorite is his SI's reaction to New Fluttershy and getting kicked out of her house after she came back from Iron Will's Seminar. He immediatly heads to Twilight's house and the first thing he says upon Twilight opening the door: ""Fluttershy has been possessed and we need to save her immortal soul."
Imagine hearing the words "Even if you are a twisted, bondage-loving masochistic bisexual nymphomaniac, we still love you." Now imagine hearing Fluttershy be the one who says that like she did here. 
So much of Six Brides for Two Sisters could qualify, but particularly the varying reactions of each of the Mane 6 finding out that Princess Luna intends to marry all of them. Also, the realization that ten years after Celestia promised to marry Twilight Sparkle when she was ready, Celestia is the only pony in Equestria who interpreted this as offering to officiate Twilight's wedding.
This exchange in Chapter 3:
Pinkie: Just think of all the parties we’ll need first! We’ll all need to have bridal showers, and bachelorette parties, and the rehearsal dinner, and the reception, and then anniversary parties for years to come, and… oh, Applejack… it’s just so wonderful. Applejack… we get to have the one kind of party I’ve never been able to have before.
Applejack: Pinkie, how in the wide world of Equestria can there still be a type of party you ain’t thrown? Y'all’ve had birthday parties, wedding parties, wakes, both swingin’ and otherwise, bachelor parties, bachelorette parties, anniversaries, bridal showers, baby showers, goin’-away parties, welcome-home parties, graduations, fake-murder-mystery parties, a real-murder-mystery party, and even that one festive search party you took charge of. Still not sure how you managed to pull that one off but the foals were found, and everypony enjoyed the gingerbread house, so Ah’ll give it to ya. Ah even remember that time you tried ta arrange an… Pinkie… no. Just… just no. Pinkie… you remember what happened when you tried to get folks to go to the first one, don’t you? The torches, and pitchforks, and effigies of you they started burnin’ before the Cakes convinced everypony you’d gotten into some special brownies they’d made, and weren’t quite right in the head when you’d sent out the invitations. Please, please tell me you remember that.
Twilight: Remember what, Applejack? What kind of party did she try to throw? A tea party at the harbor? A political party? A ritual sacrifice? Does ritual sacrifice even count as a party?
Pinkie/Applejack: An orgy!
Starting in Chapter 5, Octavia and Vinyl Scratch show up to help the Royal Sisters prepare for the wedding, but not as musicians. Instead, they're there to teach the Princesses techniques for pleasuring mares, which they proceed to do through practical demonstration. Luna is fascinated and taking notes through the whole thing while Celestia seriously considers adopting an evil persona and torching some empty buildings just so she can get banished to the sun instead.
‘I will do literally anything you want if this doesn’t happen right now,’ she promised, willing herself to ignore the madness of trying to bargain with primal forces which existed beyond thought. ‘I’ll turn Equestria into a totalitarian state dedicated to order at the cost of individuality. I’ll free Discord and embrace chaos as the natural state of things. I’ll embrace evil and bring about unending daylight,” she offered desperately. ‘Just please, please don’t make me take lessons on how to please a mare while my little sister is here with me.’ But the cosmos paid her no heed.
For some Original Flavour fantasy-slapstick, the story Study Break, in which Hilarity Ensues after Twilight unwittingly eats an enchanted apple from a tree in the Canterlot palace grounds, which causes random magical effects when she sneezes, always at the worst possible time.
Fluttershy: A pony wouldn’t just flop after being slashed like that! There would be at least some spasm or other reflex action! And the blood spray? Way too even, like someone was spraying it with a hose. It’s like Starlight didn’t even have a heartbeat, and the viscosity is just far too low for aortic blood. Has the director ever seen a severed aorta? And while I’m on the subject, how can I expect to take this seriously when there’s no evidence of trauma to her vital organs with a cut that deep? Honestly, any pony with a basic understanding of pony anatomy could see how fake this is!
Also, Rarity's "threats" to Rainbow Dash. Like when Dash threatens to start the "chimicherrychanga" rant:
Rarity: “You finish that word, punk, and I will style your hair. I mean it.” Rarity grabbed Rainbow Dash by the shoulders and forcibly turned her around, gazing with murderous intent in her target’s eyes. “I will make you beautiful! There will be curling irons involved. When I am done, I am going to wash that mane of yours, and condition it. It will be silky-smooth for weeks. Do I make myself clear?”
Or when Dash tries to join Pinkie in mentioning Rarity's embarrassing moments by bringing up the Sonic Rainboom incident:
Rarity: By Fancy's Pants, if you make a lame pun about me falling for you, head over hooves or otherwise, I will take you shoe shopping! And then I’ll get you a nice, bright, fancy dress! With sequins. Are we clear?!
Rainbow Dash (terrified): C-Crystal.
Before Fluttershy's rant, Twilight comments that Rarity apparently likes to write about Blueblood dying horribly; one particularly gruesome story involved a cider mug and a broom.
In chapter eight of My Little Mommies, Pinkie Pie is telling the Cakes about how a magic mirror created a baby by combining traits from her and Fluttershy. To Fluttershy's surprise, the Cakes pretty much accept this immediately and congratulate Pinkie.
What does Pinkie Pie leave behind for Twilight and Blueblood at the end of Royal Courtin' found here? A condom
And it turns out to be broken
This fic about Shining learning a surprising fact about his wife. How her name is actually spelled. Bonus points for what it does with the premise.
This fic features Fluttershy competing in the World Quiet Game Championships. Not only are said Championships played as Serious Business to the point thousands of fans are in attendance and Princess Celestia is the judge (much to Twilight and Rarity's shock), Fluttershy's opponents are Nightmare Moon (actually Luna in disguise to try and throw off her competition), Shy Sparrow (a dead unicorn skeleton who's Last Request was for his corpse to compete), and Angel. Rarity also enters the amateur competition and loses in a couple seconds.
Don't let the fanfic Mommy Nearest fool you with how sad it starts. Yes, it's about Rainbow Dash having a horrible accident and having brain damage, but it ends on the hilarious note of Rainbow Dash being revealed as Princess Celestia's illegitimate daughter, specifically with an earth pony. And I am going to warn you right now, if you've ruined that hilarious twist, there's one more so hilarious that I dare not put it in spoilers, it's so ridiculous.
In Halcyon Hearts, Shining Armor learns from Celestia that Twilight has finally gotten a boyfriend - a recently-paroled convict named Blaze. The story cuts to Twilight and her boyfriend enjoying their first proper date, and then towards the end of the scene:
Twilight: Do you hear something?
Blaze: No, why?
Twilight: I could have sworn I heard somepony calling my name just now...it sounded angry.
Hail to the King is just wall to wall hilarity, as a recently deceased human's soul gets diverted to inhabit the body of the recently defeated King Sombra. Everypony assumes that Sombra is still crazy, but instead of just Ax-Crazy, they think he's out of his mind.. And he isn't helping his case, particularly when trying to explain what he really is.
Shining Armor: Then how come I’ve never met one? We should be drowning in a sea of humans by now.
Cadence: Because we’re just figments of his imagination, remember? So that’s where his mind is right now. He’s a hyper-evolved, futuristic, thunder-monkey.
Past Sins has an in-progress MST of the original edit of the story, which can be found here. While it's only gotten the prologue and the first three chapters finished, with Chapters 4 to 7 currently being worked on, it's shaping up to be hilarious.
During the run-down of the two characters, Starscream's appearance in the execrable Kiss Players manga is mentioned, where he possessed a cybernetic schoolgirl while she was in the bathroom, then forgot to pull her underwear up.
Boomstick: Props to you, Japan. I did not see that one coming.
This interpretation of how the season 2 finale could have gone.
Bronies React is full of them, but one good one is in the first episode, where they're reacting to the Teens React to My Little Pony: Friendship is Magic episode. In the episode the bronies are reacting to, one of the teens is asked why they think they're being shown this, and responds with "Maybe you think I'm on the other side of the street, and I'm not?" Cue Flat "What." stares and gestures from each of the bronies. Even Solrac / Yaplap is left speechless.